Mutagenetix > Incidental Mutation

Incidental Mutation 'R5250:Hoxd3'

398910

Institutional Source

Beutler Lab

Gene Symbol

Hoxd3

Ensembl Gene

ENSMUSG00000079277

Gene Name

homeobox D3

Synonyms

Hox-5.5, Hox-4.1

MMRRC Submission

042821-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.823) question?

Stock #

R5250 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

74542337-74578615 bp(+) (GRCm39)

Type of Mutation

nonsense

DNA Base Change (assembly)

C to T at 74574650 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamine to Stop codon at position 99 (Q99*)

Ref Sequence

ENSEMBL: ENSMUSP00000107614 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000047830] [ENSMUST00000053932] [ENSMUST00000111982] [ENSMUST00000111983] [ENSMUST00000140666] [ENSMUST00000144544]

AlphaFold

P09027

Predicted Effect

probably null
Transcript: ENSMUST00000047830
AA Change: Q99*

SMART Domains

Protein: ENSMUSP00000044809
Gene: ENSMUSG00000079277
AA Change: Q99*

Domain	Start	End	E-Value	Type
low complexity region	93	135	N/A	INTRINSIC
low complexity region	141	159	N/A	INTRINSIC
HOX	195	257	5.83e-28	SMART
Pfam:DUF4074	369	431	8.9e-35	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000053932

SMART Domains

Protein: ENSMUSP00000051355
Gene: ENSMUSG00000100642

Domain	Start	End	E-Value	Type
low complexity region	93	135	N/A	INTRINSIC
low complexity region	141	159	N/A	INTRINSIC
HOX	195	257	5.83e-28	SMART
Pfam:DUF4074	370	431	1.4e-33	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000100000

Predicted Effect

probably null
Transcript: ENSMUST00000111982
AA Change: Q99*

SMART Domains

Protein: ENSMUSP00000107613
Gene: ENSMUSG00000079277
AA Change: Q99*

Domain	Start	End	E-Value	Type
low complexity region	93	135	N/A	INTRINSIC
low complexity region	141	159	N/A	INTRINSIC
HOX	195	257	5.83e-28	SMART
Pfam:DUF4074	369	431	8.9e-35	PFAM

Predicted Effect

probably null
Transcript: ENSMUST00000111983
AA Change: Q99*

SMART Domains

Protein: ENSMUSP00000107614
Gene: ENSMUSG00000079277
AA Change: Q99*

Domain	Start	End	E-Value	Type
low complexity region	93	135	N/A	INTRINSIC
low complexity region	141	159	N/A	INTRINSIC
HOX	195	257	5.83e-28	SMART
Pfam:DUF4074	369	431	8.9e-35	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000140666

SMART Domains

Protein: ENSMUSP00000134616
Gene: ENSMUSG00000079277

Domain	Start	End	E-Value	Type
HOX	35	97	5.83e-28	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000144544

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000190553

Meta Mutation Damage Score

0.9713

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.9%
20x: 94.4%

Validation Efficiency

100% (60/60)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene belongs to the homeobox family of genes. The homeobox genes encode a highly conserved family of transcription factors that play an important role in morphogenesis in all multicellular organisms. Mammals possess four similar homeobox gene clusters, HOXA, HOXB, HOXC and HOXD, located on different chromosomes, consisting of 9 to 11 genes arranged in tandem. This gene is one of several homeobox HOXD genes located at 2q31-2q37 chromosome regions. Deletions that removed the entire HOXD gene cluster or 5' end of this cluster have been associated with severe limb and genital abnormalities. The protein encoded by this gene may play a role in the regulation of cell adhesion processes. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a knock-out allele show partial postnatal lethality, asymmetric rib-sternum attachment, and anterior transformations of the cervical vertebrae I (atlas) and II (axis). Mice homozygous for a different knock-out allele lack the anteriorarch of the atlas and the dens of the axis. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 52 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adamtsl1	A	T	4: 86,135,182 (GRCm39)	K236*	probably null	Het
Adgre5	A	G	8: 84,460,069 (GRCm39)	V109A	probably benign	Het
Adora2a	T	C	10: 75,161,882 (GRCm39)	I7T	probably damaging	Het
Ankrd6	A	G	4: 32,860,335 (GRCm39)	V36A	probably damaging	Het
Arhgef2	T	C	3: 88,540,955 (GRCm39)		probably null	Het
Atg14	G	A	14: 47,805,656 (GRCm39)	R70C	probably damaging	Het
Atg2b	G	A	12: 105,602,024 (GRCm39)	R1651W	probably damaging	Het
Atp6v0a1	T	A	11: 100,933,870 (GRCm39)	V553D	possibly damaging	Het
Bard1	G	A	1: 71,113,722 (GRCm39)	L420F	probably damaging	Het
Bcat1	C	G	6: 144,993,165 (GRCm39)		probably null	Het
Bpifb5	A	T	2: 154,066,881 (GRCm39)	N45Y	probably benign	Het
Btbd17	G	T	11: 114,682,234 (GRCm39)		probably benign	Het
Ccdc24	T	C	4: 117,726,826 (GRCm39)	T296A	possibly damaging	Het
Col11a1	A	G	3: 114,010,819 (GRCm39)		probably benign	Het
Cspg4b	A	G	13: 113,456,305 (GRCm39)	N784D	possibly damaging	Het
Dhx38	A	T	8: 110,283,152 (GRCm39)	V555D	probably damaging	Het
Dixdc1	T	G	9: 50,595,035 (GRCm39)	E230A	possibly damaging	Het
Dnah7b	T	G	1: 46,412,514 (GRCm39)	V4041G	probably damaging	Het
Dnhd1	A	T	7: 105,334,968 (GRCm39)	I1021L	probably damaging	Het
Fgl2	A	G	5: 21,580,521 (GRCm39)	S288G	possibly damaging	Het
Flt4	T	A	11: 49,521,227 (GRCm39)	I412N	possibly damaging	Het
Gabrb1	A	G	5: 72,026,922 (GRCm39)	I141V	possibly damaging	Het
Gpc2	A	G	5: 138,277,230 (GRCm39)	Y66H	probably damaging	Het
Inpp5d	T	C	1: 87,637,397 (GRCm39)	V781A	probably damaging	Het
Larp4b	T	C	13: 9,221,013 (GRCm39)		probably benign	Het
Lrrfip1	T	A	1: 91,043,618 (GRCm39)	S674R	possibly damaging	Het
Megf6	A	G	4: 154,340,467 (GRCm39)	T561A	possibly damaging	Het
Mpo	A	T	11: 87,694,259 (GRCm39)	Q83L	probably benign	Het
Mucl2	T	C	15: 103,927,733 (GRCm39)	N75D	possibly damaging	Het
Myh13	C	T	11: 67,218,085 (GRCm39)	Q53*	probably null	Het
Myot	T	A	18: 44,479,137 (GRCm39)	D291E	probably damaging	Het
Nae1	A	G	8: 105,257,023 (GRCm39)		probably null	Het
Ncoa2	A	T	1: 13,294,913 (GRCm39)	S2R	probably damaging	Het
Nktr	T	A	9: 121,578,858 (GRCm39)		probably benign	Het
Nrxn1	A	G	17: 90,842,869 (GRCm39)		probably benign	Het
Or10aa3	T	G	1: 173,878,838 (GRCm39)	F300V	probably benign	Het
Or14j4	A	G	17: 37,920,851 (GRCm39)	S264P	probably damaging	Het
Or5an1b	T	C	19: 12,299,430 (GRCm39)	T254A	probably benign	Het
P2rx2	T	C	5: 110,489,454 (GRCm39)	E160G	probably damaging	Het
Pcdhga11	A	T	18: 37,890,990 (GRCm39)	D666V	probably damaging	Het
Pcm1	A	T	8: 41,765,242 (GRCm39)	E1484D	probably damaging	Het
Pdia4	C	T	6: 47,773,619 (GRCm39)	A577T	possibly damaging	Het
Potefam1	T	G	2: 111,058,422 (GRCm39)	T124P	possibly damaging	Het
Ppm1e	T	C	11: 87,121,744 (GRCm39)	I738V	probably benign	Het
Ppp1r13b	G	T	12: 111,811,394 (GRCm39)	R165S	probably benign	Het
Rasgrp2	T	C	19: 6,454,343 (GRCm39)	W129R	probably damaging	Het
Smurf2	A	G	11: 106,747,005 (GRCm39)		probably null	Het
Spmap1	C	A	11: 97,663,553 (GRCm39)	W99L	possibly damaging	Het
Ubr2	G	T	17: 47,241,368 (GRCm39)	Q1729K	probably benign	Het
Zfp260	T	A	7: 29,804,392 (GRCm39)	H97Q	probably damaging	Het
Zfp429	G	T	13: 67,538,638 (GRCm39)	R269S	probably benign	Het
Zfp568	T	C	7: 29,716,655 (GRCm39)	V185A	probably benign	Het

Other mutations in Hoxd3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02636:Hoxd3	APN	2	74,577,298 (GRCm39)	missense	probably benign	0.32
IGL03017:Hoxd3	APN	2	74,577,050 (GRCm39)	missense	possibly damaging	0.68
candide	UTSW	2	74,574,420 (GRCm39)	missense	probably damaging	1.00
compressed	UTSW	2	74,574,650 (GRCm39)	nonsense	probably null
R1977:Hoxd3	UTSW	2	74,574,620 (GRCm39)	missense	possibly damaging	0.94
R2079:Hoxd3	UTSW	2	74,574,610 (GRCm39)	missense	probably damaging	0.97
R2124:Hoxd3	UTSW	2	74,574,578 (GRCm39)	missense	possibly damaging	0.92
R5143:Hoxd3	UTSW	2	74,576,716 (GRCm39)	missense	probably damaging	1.00
R5256:Hoxd3	UTSW	2	74,577,211 (GRCm39)	missense	possibly damaging	0.88
R5943:Hoxd3	UTSW	2	74,577,173 (GRCm39)	missense	probably benign	0.00
R6300:Hoxd3	UTSW	2	74,574,420 (GRCm39)	missense	probably damaging	1.00
R7362:Hoxd3	UTSW	2	74,574,563 (GRCm39)	missense	possibly damaging	0.59
R9203:Hoxd3	UTSW	2	74,576,744 (GRCm39)	missense	probably damaging	0.99

Predicted Primers

PCR Primer
(F):5'- AGCCACTGACACATATGGC -3'
(R):5'- TCGGGATTCTTTCATCCAGGG -3'

Sequencing Primer
(F):5'- TATGGCTACAGCACTCCTCATCAG -3'
(R):5'- GATTCTTTCATCCAGGGGAAGATC -3'

Posted On

2016-07-06